***In 2000 a number of scientists had started to reassess the hypothesis of an Asian origin of the YAP insertion. Underhill et al. 2000 identified the D-M174 mutation that defines haplogroup D. The M174 allele is found in the ancestral state in all African lineages including haplogroup E. The discovery of M174 mutation meant that haplogroup E could not be a subclade of haplogroup D. These findings effectively neutralized the argument of an Asian origin of the YAP+ based on the character state of the M40 and M96 mutations that define haplogroup E. According to Underhill et al. 2000, the M174 data alone would support an African origin of the YAP insertion.

Further arguments were made supporting and African origin of the YAP in Underhill et al. 2001. The arguments for an African origin include.

1. Africa has the highest frequency of YAP (>80%) Haplogroup DE is often referred to by the most well-known unique event polymorphism (UEP) which defines it, the Y-chromosome Alu Polymorphism (YAP). The YAP mutation was caused when a strand of DNA called Alu, which copies itself, inserted a copy into the Y chromosome. A Y chromosome that has the YAP mutation is called YAP-positive (YAP+), and a Y chromosome that does not have the YAP mutation is labeled YAP-negative (YAP-). Haplogroup DE is an estimated 65,000 years old.. Whereas the YAP+ in Asia has a fairly restricted geographic distribution, mainly at low to moderate frequencies (average 9.6%) in East Asia.

2. It was claimed that there was no archaeological evidence of a back-migration to Africa, and at the time of writing that there was no unequivocal Y DNA, mitochondrial DNA or autosomal DNA evidence of a back migration to Africa.

3. Although Haplogroup C seems to have originated in Asia at a similar time to Haplogroup DE's origin, Haplogroup C shows no sign of back migration to Africa.

The debate concerning the mechanisms underlying the prehistoric spread of farming to Southeast Europe is framed around the opposing roles of population movement and cultural diffusion. To investigate the possible involvement of local people during the transition of agriculture in the Balkans, we analysed patterns of Y-chromosome diversity in 1206 subjects from 17 population samples, mainly from Southeast Europe. Evidence from three Y-chromosome lineages, I-M423, E-V13 and J-M241, make it possible to distinguish between Holocene Mesolithic forager and subsequent Neolithic range expansions from the eastern Sahara and the Near East, respectively. In particular, whereas the Balkan microsatellite variation associated to J-M241 correlates with the Neolithic period, those related to E-V13 and I-M423 Balkan Y chromosomes are consistent with a late Mesolithic time frame. In addition, the low frequency and variance associated to I-M423 and E-V13 in Anatolia and the Middle East, support an European Mesolithic origin of these two clades. Thus, these Balkan Mesolithic foragers with their own autochthonous genetic signatures, were destined to become the earliest to adopt farming, when it was subsequently introduced by a cadre of migrating farmers from the Near East. These initial local converted farmers became the principal agents spreading this economy using maritime leapfrog colonization strategies in the Adriatic and transmitting the Neolithic cultural package to other adjacent Mesolithic populations. The ensuing range expansions of E-V13 and I-M423 parallel in space and time the diffusion of Neolithic Impressed Ware, thereby supporting a case of cultural diffusion using genetic evidence.

Differential Y-chromosome Anatolian influences on the Greek and Cretan Neolithic

The earliest Neolithic sites of Europe are located in Crete and mainland Greece. A debate persists concerning whether these farmers originated in neighboring Anatolia and the role of maritime colonization. To address these issues 171 samples were collected from areas near three known early Neolithic settlements in Greece together with 193 samples from Crete. An analysis of Y-chromosome haplogroups determined that the samples from the Greek Neolithic sites showed strong affinity to Balkan data, while Crete shows affinity with central/Mediterranean Anatolia. Haplogroup J2b-M12 was frequent in Thessaly and Greek Macedonia while haplogroup J2a-M410 was scarce. Alternatively, Crete, like Anatolia showed a high frequency of J2a-M410 and a low frequency of J2b-M12. This dichotomy parallels archaeobotanical evidence, specifically that while bread wheat (Triticum aestivum) is known from Neolithic Anatolia, Crete and southern Italy; it is absent from earliest Neolithic Greece. The expansion time of YSTR variation for haplogroup E3b1a2-V13, in the Peloponnese was consistent with an indigenous Mesolithic presence. In turn, two distinctive haplogroups, J2a1h-M319 and J2a1b1-M92, have demographic properties consistent with Bronze Age expansions in Crete, arguably from NW/W Anatolia and Syro-Palestine, while a later mainland (Mycenaean) contribution to Crete is indicated by relative frequencies of V13.

"Tracing Past Human Male Movements in Northern/Eastern Africa and Western Eurasia: New Clues from Y-Chromosomal Haplogroups E-M78 and J-M12"

...Recent studies of the Neolithic paternal haplogroups E (M78) and J1 (M267) and J2 (M172) strongly suggest continuous Mesolithic, Neolithic and post-Neolithic gene flows within southeastern Europe and between Europe and the Near East in both directions.

The Neolithic haplogroup E (M78) is represented in Europe by its internal lineages E3b1a and E3b1a2 (E-V13 polymorphism). It constitutes about 85% of the European E-M78 chromosomes, with a clinal pattern of frequency distribution from the southern Balkan Peninsula (19.6%) to west Europe (2.5%). This haplogroup reached the southern Balkans after 17000calBP and its phylogeny reveals signatures of several demographic population expansions within Europe.

Cruciani et al. (2007), Pompei et al. (2008) and King et al. (2008) agree that the earliest expansion was linked to Mesolithic demographic expansion from western Asia into Europe, and that the later series of Neolithic and Bronze Age expansions were restricted regionally within southeastern Europe. Thus the first demographic expansion within Europe, from the Peloponnese to Thessaly and Greek Macedonia, was calculated at 8600 calBP (King et al. 2008, 211).

All of the demographic expansion within the Balkans of the later haplogroups, E3b1a and E3b1a2, post-date the transition to farming in the region. The haplogroup J is subdivided into two major subhaplogroups, J1 (M267) and J2 (M172). The latter was hypothesised as representing an important signature of Neolithic demic diffusion and to have been associated with the appearance of painted pottery and figurines. It became clear recently that it mainly constitutes the signatures of several post Neolithic expansions within Europe and not demic diffusion into Europe. The J2 subclade frequencies in southeastern Europe show two distinct clusters. While the J2a (M410) subclades are frequent in the Peloponnese, Crete and Anatolia, but rare in the Balkans, the J2b (M12) subclades are, conversely, the most frequent in the Balkans and in the Mediterranean (King et al. 2008; Battaglia et al. 2009). The expansion time for the J2b (M12) sub-haplogroup and associated migration from the southern Balkans toward the Carpathian basin is consistent with the Late Neolithic (King et al. 2008, 209). The geographical origin of the J2b subclade remains unknown, although it shows a trend of decreasing frequency from the Balkans (7-9%) to Anatolia (1.7%) (King et al. 2008). Interestingly, in the region where the PPNA-C sites at Çayönü, Göbekli Tepe and Hallan Çemi are located, the 4.7% clade frequency is significantly lower than those in the Balkans. Barać et al. (2003) and Peričić et al. (2005; 2006) recently observed that a lower frequency of sub-haplogroups J2b and E3b1 significantly distinguishes the populations of the western Balkans and the Adriatic (7.9%) from neighbouring populations of the Vardar-Morava river system in the eastern Balkans (21.9%).

This corresponds with the recently identified pre-Neolithic I haplogroup and its subclade I1b* (I2a2–M423 after Underhill et al. 2005) with a frequency distribution that reaches a maximum in the western Balkans, the Adriatic (52%-64%) and the central Balkans (<70%). Haplogroup I is the only haplogroup almost entirely restricted to the European continent. It appeared in Europe, probably before the Last Glacial Maximum, with frequency peaks of reached in two distinct regions - in the Nordic populations of Scandinavia and in the Balkan populations of Southern Europe. Subhaplogroup I1b* expanded from a refuge in southeastern Europe before the Neolithic and a gene flow from the Balkans to Anatolia has also been suggested (Semino et al. 2000; Barać et al. 2003; Rootsi et al. 2004; 2006; Cinnioğlu et al. 2004; Peričić et al. 2005; 2006; Battaglia 2009) (Fig. 3).

Geneticists suggest that the peopling of Europe was a complex process, and that the view of the spread of the Neolithic in Europe as a result of a single, unique and homogeneous process is too simplistic. The paternal heritage of southeastern Europe reveals that the region was both an important source and recipient of continuous gene flow. In addition, the low frequency and variance associated with I (M423) and E (V13) in Anatolia and the Middle East support the European Mesolithic origin of these two clades. The Neolithic and post Neolithic component in the gene pool is most clearly marked by the presence of the J (M241) lineage and its expansion signals associated with Balkan microsatellite variation. Its frequency in south-east European populations ranges from 2% to 20%. The remaining genetic variations are associated with pre-Neolithic hunter-gatherer haplogroups E, I and R....

Ancient DNA suggests the leading role played by men in the Neolithic dissemination (2011)

Marie Lacan

Abstract

The impact of the Neolithic dispersal on the western European populations is subject to continuing debate. To trace and date genetic lineages potentially brought during this transition and so understand the origin of the gene pool of current populations, we studied DNA extracted from human remains excavated in a Spanish funeral cave dating from the beginning of the V millennium BC. Thanks to a “multimarkers” approach based on the analysis of mitochondrial and nuclear DNA (autosomes and Y-chromosome), we obtained information on the early Neolithic funeral practices and on the bio-geographical origin of the inhumed individuals. No close kinship was detected. Maternal haplogroups found are consistent with pre-Neolithic settlement, whereas the Y-chromosomal analyses permitted confirmation of the existence in Spain approximately 7.000 y ago of two haplogroups previously associated with the Neolithic transition: G2a and E1b1b1a1b. These results are highly consistent with those previously found in Neolithic individuals from French Late Neolithic individuals, indicating a surprising temporal genetic homogeneity in these groups. The high frequency of G2a in Neolithic samples in western Europe could suggest, furthermore, that the role of men during Neolithic dispersal could be greater than currently estimated.

It is still unclear when haplogroup E first entered Europe. The earliest known prehistoric sample to date is an E-V13 from Catalonia dating from 5000 BCE. So we know for sure that E1b1b was present in southern Europe at least since the Early Neolithic. Nonetheless, the possibility of other migrations of E1b1b to southern Europe during the Mesolithic or Late Palaeolithic cannot be ruled out.

E-V13 is one of the major markers of the Neolithic diffusion of farming from the Balkans to central, eastern and western Europe. Like all the other subclades of E-M78, E-V13 originated in north-east Africa toward the end of the last Ice Age. Its frequency is now far higher in Greece, South Italy and the Balkans than anywhere else either because E-V13 migrated directly from North Africa to southern Europe (see framed explanation above) or due to a founder effect among the Neolithic colonisers from the southern Levant. Archeological evidence shows that the region of Thessaly, in northern Greece, was the starting point (circa 6,000 BCE) for the diffusion of agriculture through the Balkans and the Danube basin, which spread as far as west as northern France, and as far east as southwestern Russia. The modern distribution of E-V13 hints at a strong correlation with the Neolithic and Chalcolithic cultures of Old Europe, such as the Vinča, Boian (aka Giuleşti-Marişa), and Karanovo, cultures. The genetic testing of three male samples from the Linear Pottery culture (LBK) only revealed the presence of haplogroups F and G2a. The sample size was nevertheless too small to rule out that E1b1b was part of this culture. E-V13 was later associated with the ancient Greek expansion and colonisation. Outside of the Balkans and Central Europe, it is particularly common in southern Italy, Cyprus and southern France, all part of the Classical ancient Greek world.

***

"The earliest Neolithic sites of Europe are located in Crete and mainland Greece. A debate persists concerning whether these farmers originated in neighboring Anatolia and the role of maritime colonization. To address these issues 171 samples were collected from areas near three known early Neolithic settlements in Greece together with 193 samples from Crete. An analysis of Y-chromosome haplogroups determined that the samples from the Greek Neolithic sites showed strong affinity to Balkan data, while Crete shows affinity with central/ Mediterranean Anatolia. Haplogroup J2b-M12 was frequent in Thessaly and Greek Macedonia while haplogroup J2a-M410 was scarce. Alternatively, Crete, like Anatolia showed a high frequency of J2a-M410 and a low frequency of J2b-M12. This dichotomy parallels archaeobotanical evidence, specifically that while bread wheat (Triticum aestivum) is known from Neolithic Anatolia, Crete and southern Italy; it is absent from earliest Neolithic Greece. The expansion time of YSTR variation for haplogroup E3b1a2-V13, in the Peloponnese was consistent with an indigenous Mesolithic presence. In turn, two distinctive haplogroups, J2a1h-M319 and J2a1b1-M92, have demographic properties consistent with Bronze Age expansions in Crete, arguably from NW/W Anatolia and Syro-Palestine, while a later mainland (Mycenaean) contribution to Crete is indicated by relative frequencies of V13"

***

Y-chromosomal evidence of the cultural diffusion of agriculture in Southeast Europe (2008)

The debate concerning the mechanisms underlying the prehistoric spread of farming to Southeast Europe is framed around the opposing roles of population movement and cultural diffusion. To investigate the possible involvement of local people during the transition of agriculture in the Balkans, we analysed patterns of Y-chromosome diversity in 1206 subjects from 17 population samples, mainly from Southeast Europe. Evidence from three Y-chromosome lineages, I-M423, E-V13 and J-M241, make it possible to distinguish between Holocene Mesolithic forager The Mesolithic began with the Holocene warm period around 11.660 BP and ended with the introduction of farming and subsequent Neolithic range expansions from the eastern Sahara and the Near East, respectively. In particular, whereas the Balkan microsatellite variation associated to J-M241 correlates with the Neolithic period, those related to E-V13 and I-M423 Balkan Y chromosomes are consistent with a late Mesolithic time frame. In addition, the low frequency and variance associated to I-M423 and E-V13 in Anatolia and the Middle East, support an European Mesolithic origin of these two clades. Thus, these Balkan Mesolithic foragers with their own autochthonous genetic signatures, were destined to become the earliest to adopt farming, when it was subsequently introduced by a cadre of migrating farmers from the Near East. These initial local converted farmers became the principal agents spreading this economy using maritime leapfrog colonization strategies in the Adriatic and transmitting the Neolithic cultural package to other adjacent Mesolithic populations. The ensuing range expansions of E-V13 and I-M423 parallel in space and time the diffusion of Neolithic Impressed Ware, thereby supporting a case of cultural diffusion using genetic evidence.

The earliest Neolithic sites of Europe are located in Crete and mainland Greece. A debate persists concerning whether these farmers originated in neighboring Anatolia and the role of maritime colonization. To address these issues 171 samples were collected from areas near three known early Neolithic settlements in Greece together with 193 samples from Crete. An analysis of Y-chromosome haplogroups determined that the samples from the Greek Neolithic sites showed strong affinity to Balkan data, while Crete shows affinity with central/Mediterranean Anatolia. Haplogroup J2b-M12 was frequent in Thessaly and Greek Macedonia while haplogroup J2a-M410 was scarce. Alternatively, Crete, like Anatolia showed a high frequency of J2a-M410 and a low frequency of J2b-M12. This dichotomy parallels archaeobotanical evidence, specifically that while bread wheat (Triticum aestivum) is known from Neolithic Anatolia, Crete and southern Italy; it is absent from earliest Neolithic Greece. The expansion time of YSTR variation for haplogroup E3b1a2-V13, in the Peloponnese was consistent with an indigenous Mesolithic presence. In turn, two distinctive haplogroups, J2a1h-M319 and J2a1b1-M92, have demographic properties consistent with Bronze Age expansions in Crete, arguably from NW/W Anatolia and Syro-Palestine, while a later mainland (Mycenaean) contribution to Crete is indicated by relative frequencies of V13.

Outside Europe, E1b1b is found at high frequencies in Morocco (over 80%), Somalia (80%), Ethiopia (40% to 80%), Tunisia (70%), Algeria (60%), Egypt (40%), Jordan (25%), Palestine (20%) and Lebanon (17.5%). On the European continent it has the highest concentration in Kosovo (over 45%), Albania and Montenegro (both 27%), Bulgaria (23%), Macedonia and Greece (both 21%), Cyprus (20%), Sicily (20%), South Italy (18.5%), Serbia (18%) and Romania (15%).Distribution of haplogroup E1b1b in Europe, the Near East and North Africa

Origins and History

Haplogroup E1b1b (formerly E3b) represents the last major direct migration from Africa into Europe. It is believed to have first appeared in the Horn of Africa approximately 26,000 years ago and dispersed to North Africa and the Near East during the late Paleolithic and Mesolithic periods. E1b1b lineages are closely linked to the diffusion of Afroasiatic languages.

The highest genetic diversity of haplogroup E1b1b is observed in Northeast Africa, especially in Ethiopia and Somalia, which also have the monopoly of older and rarer branches like M281, V6 or V92. Ethiopians and Somalians belong mostly to the V22 and V32 (downstream of V12) subclades, but possess also a minority of M81, M123 and V42 subclades. Among the main subclades of E1b1b only V13 and V65 are absent from the Horn of Africa and probably originated in northern Africa (V65) or the southern Levant (V13).

Haplogroup E1b1b may well have been associated with the earliest development of Neolithic lifestyle and the advent of agriculture, which is so far believed to have arisen in the Fertile Crescent, but could have developed earlier in parts of Northeast Africa now covered by the Sahara desert. Agriculture spread from the Near East to Europe, at first mostly ovicaprid (domestic sheep or goat) and cattle herders. E1b1b men (accompanied by G2a, J and T men) appear to have been associated at least with the diffusion of Neolithic painted pottery from the Levant to the Balkans (Thessalian Neolithic) and with the Cardium Pottery culture (5000-1500 BCE) in the Western Mediterranean. The only concrete evidence for this at the moment is the presence of the E-V13 subclade, commonest in the southern Balkans today, at a 7000-year old Neolithic site in north-east Spain, which was tested by Lacan et al (2011). The African origin of some Neolithic cattle was confirmed by Decker et al (2013), who reported that Iberian and Italian cattle possess introgression from African taurine.

Judging from modern frequencies, E1b1b would have been a major Near Eastern haplogroup linked to the propagation of agriculture in Europe. It is the only Near Eastern haplogroup consistently found throughout Europe, even in Norway, Sweden, Finland and Baltic countries, which are conspicuous by the absence of other Neolithic haplogroups like G2a (bar the Indo-European G2a3b1), J1 and T (except in Estonia).

E1b1b lineages would have been part and parcel to virtually all Neolithic and subsequent cultures in Europe, if only as a tiny minority in Scandinavia, Northeast Europe and in the Pontic Steppe. Although E1b1b represents the last major migration out of Africa, E1b1b individuals may have been among the first people to have acquired the alleles for fair skin. European hunter-gatherers were still dark skinned as recently as 7000 years ago (Olalde et al. 2014), while the Early Neolithic farmers from the Near East possessed alleles for fair skin found in modern Europeans. Those Neolithic farmers would have included members of haplogroup E-V13 (confirmed) as well as E-M34 (inferred). It is still unclear exactly when and among which haplogroup fair skin arose, but it has been suggested that the new diet brought by cereral agriculture would have caused deficiencies in vitamin D, which was traditionally absorbed from fish and meat among foragers. Mutations for light skin would have been positively selected among Neolithic agriculturalists to stimulate the production of vitamin D from sunlight in order to compensate for the scarcity of meat. So ironically the first white-skinned Europeans may have been farmers partially descended from people recently arrived from Northeast Africa.

Expansion of agriculture from the Middle East to Europe (9500-3800 BCE)

The ancient Greeks contributed to the diffusion of E1b1b to places such as Cyprus, Sicily, southern Italy, Liguria, Provence and eastern Spain, while the Phoenicians and Carthaginians brought more E1b1b to Cyprus, Malta, Sicily, Sardinia, Ibiza and southern Iberia. Migrations within the Roman Empire probably played a role, although a minor one, in the redistribution of E1b1b in Europe.Did E1b1b cross directly from North Africa to Europe due to climate change?

It is still unclear when haplogroup E first entered Europe. The earliest known prehistoric sample to date is an E-V13 from Catalonia dating from 5000BCE. So we know for sure that E1b1b was present in southern Europe at least since the Early Neolithic. Nonetheless, the possibility of other migrations of E1b1b to southern Europe during the Mesolithic or Late Palaeolithic cannot be ruled out.

E1b1b in Iberia

It is highly probable that the E-M81 subclade, most commonly found in Northwest Africa, settled in Iberia before Neolithic herders from the Cardium Pottery culture arrived. Nowadays E-M81 is far more frequent in western Iberia than anywhere else in Europe or the Near East. One could argue that E-M81 came during the Moorish occupation of Spain during the Middle Ages. But then E-M81 would be found chiefly in southern Iberia, and certainly not in the north-west, which was never conquered by the Muslims. Actually the highest percentage of M81 is Iberia is found in the northern region of Cantabria, the most sheltered place in the peninsula, which has been inhabited continuously since the Paleolithic. Modern Cantabrians belong overwhelmingly to mtDNA lineages H, HV, V and U5, and of three samples tested from Palaeolithic Cantabria all belong to one of these haplogroups, a sign of genetic continuity hinting that E-M81 could already have been present in the region back then.

Besides, Neolithic sites in Spain have yielded several samples of African mtDNA (e.g. L1b1 in Andalusia, L2 in the Basque Country and L3 Valencia). L1b1 is specific to West Africa and could not have come with Near Eastern farmers. Consequently, E-M81 must have come to Iberia at latest during the Neolithic. However, since no Neolithic culture is known to have originated in the Maghreb, it would make more sense if E-M81 came during the Late Paleolithic.

At the Last Glacial Maximum, sea levels were 120 metres lower than today and the Strait of Gibraltar was just a few kilometres wide, permitting even the most primitive raft to cross it easily. Is it merely a coincidence that the last attested trace of Neanderthal in Iberia (actually in Gibraltar itself) dates from 24,000 years ago, a short time before the Last Glacial Maximum? Could their disappearance be the result of an an absorption by Homo Sapiens from North Africa? The last Iberian Neanderthals did show some signs of hybridization with Homo Sapiens. Whereas Homo Sapiens indisputably colonised Paleolithic Europe from the Near East, a counter-current colonisation from Northwest Africa is plausible too.

E1b1b in South Italy and the Balkans

One might wonder why E1b1b is more common in the southern Balkans (Greece included) and southern Italy than anywhere in the Near East, except in Egypt. What's more, the dominant form of E1b1b in Southeast Europe is E-V13, a subclade absent from the Horn of Africa and only present at low frequencies in North Africa (peaking in Lybia), the Levant and western Anatolia. It is usually assumed that E-V13 and other E1b1b lineages came to the Balkans from the southern Levant via Anatolia during the Neolithic and that the high frequency of E-V13 was caused by a founder effect among the colonisers. An alternate hypothesis is that E-V13 migrated directly from North Africa to southern Europe, crossing the Mediterranean from Tunisia to Sicily, then to Italy and to the southern Balkans.

The Sahara changed many times from a lush green place to a hot and arid desert in the last 20000 years. It was as arid as today at the end of the last Ice Age 13000 years ago, then the warming climate brought tropical monsoons again from 10000 to 7000 years before present. The desertification taking place today started around 6200 years ago. This series of severe transformations of their environment surely had a tremendous effect on the indigenous (E1b1b) people, causing populations booms during the green millennia following the Last Glacial Maximum, then again during the Neolithic period and prompting migrations to milder climes once the rain had gone. The region most affected by the desertification would have been around modern Libya. The northern Maghreb enjoys the protection of the mountains that stopped the advance of the desert. Egypt had the Nile and its delta. As a result, if desertification did prompt North Africans to cross the Mediterranean at one time or another, they would most probably have crossed to Sicily first.

In such a scenario, North Africans would have belonged primarily to haplogroup E-V13, but might have carried other subclades too, including E-M81. If a founder effect caused the higher frequency of E-V13 in Europe it would have taken place during the migration from Africa to Sicily. That would explain why E-V13 is more common in Lybia today than anywhere in the Near East, and why E-M81 is found in Italy and the Balkans. The small presence of E-V13 (and perhaps even E-M81) in the Near East that could be explained by the extremely long Greek presence in the eastern Mediterranean from the time of Alexander the Great until the end of the Byzantine domination over the region during the Middle Ages.

The strongest evidence in favour of E1b1b crossing directly from North Africa to southern Italy is that it has more African admixture than the Balkans, Greece or Anatolia. This is true of the Northwest African admixture and the East African (Red sea) admixture.

The Neolthic farmers who migrated from the southern Levant to the Balkans would have brought mostly Southwest Asian admixture with such lineages as E-M34, E-V22, E-V12, G2a, J1 and T, and perhaps some more E-V13 too. The elevated incidence of E1b1b in the Balkans, Greece and South Italy would therefore have two different origins: a first migration from Tunsia to South Italy then to the Balkans during the Late Paleolithic and the later migration of Levantine herders and farmers via Anatolia during the Early Neolithic. The Thessalian Neolithic would have emerged, like in many other places, as fusion of Near Eastern immigrants and indigenous ones. In this case both might have carried a considerable percentage of E1b1b lineages.

The hypothesis of E1b1b settling Italy and the Balkans since the Late Paleolithic would also explain:

1) ... why South Italians are remarkably dolicocephalic (long-headed) like North Africans (and Iberians), while North Italians are quite brachycephalic (broad-headed) like Central Europeans and Eastern Europeans and West Asians. A direct migration from North Africa to South Italy would have resulted not only in higher African admixture in South Italians, but also in a similar morphology. The Greeks are intermediary because they would have been blended with broad-headed West Asian Neolithic farmers. Further north in the Balkans the broad head shape won over time thanks to the combined West Asian and Eastern European (including Indo-European) migrations.

2) the almost complete absence of other Paleolithic lineage (notably I2) from southern and central Italy, except in Sardinia, which was presumably not settled by Paleolithic North Africans due to its distance from the nearest coast. The same applies to Greece, Macedonia, Albania, etc. where I2a1b lineages only came between the Bronze Age (Thracians, Illyrians) and the Middle Ages (Slavs). Why would indigenous Paleolithic lineages be wiped out from the Balkans and most of Italy with the arrival of Near Eastern farmers, but survived and remained the dominant lineage in Sardinia, which was an important Neolithic centre belonging to the same Cardium Pottery culture as the rest of Italy? The best explanation is that E1b1b was already the dominant Paleolithic lineage in the Balkans and Italy apart from Sardinia, and therefore wasn't wiped out at all.

Subclades

Five major subclades of E1b1b (V12, V13, V22, M81, M123) originated in Northeast Africa before the Neolithic. Consequently most of them are present virtually in all regions where E1b1b is found. One exception is Norway, Sweden and Finland, where only E-V13 seems to be present.The frequency of E subclades has varied geographically over time due to founder effects in Neolithic populations, i.e. the migration of a small group of settlers carrying among whom one paternal lineage was much more common than any others. Examples of founder effects include E-V12 in southern Egypt, E-V13 in the Balkans, E-V32 in Somalia, E-V65 on the Mediterranean coast of Africa, and E-M81 in Northwest Africa.

E1b1b1a1 (M78)

E-M78 is the most common variety of haplogroup E among Europeans and Near Easterners. E-M78 is divided into 4 main branches: E1b1b1a1 (E-V12), E1b1b1a2 (E-V13), E1b1b1a3 (E-V22) and E1b1b1a4 (E-V65), each subdivided in further subclades.

E-V13 is one of the major markers of the Neolithic diffusion of farming from the Balkans to central, eastern and western Europe. Like all the other subclades of E-M78, E-V13 originated in north-east Africa toward the end of the last Ice Age. Its frequency is now far higher in Greece, South Italy and the Balkans than anywhere else either because E-V13 migrated directly from North Africa to southern Europe (see framed explanation above) or due to a founder effect among the Neolithic colonisers from the southern Levant. Archeological evidence shows that the region of Thessaly, in northern Greece, was the starting point (circa 6000 BCE) for the diffusion of agriculture through the Balkans and the Danube basin, which spread as far as west as northern France, and as far east as southwestern Russia. The modern distribution of E-V13 hints at a strong correlation with the Neolithic and Chalcolithic cultures of Old Europe, such as the Vinča, Boian (aka Giuleşti-Marişa) and Karanovo, cultures. The genetic testing of three male samples from the Linear Pottery culture (LBK) only revealed the presence of haplogroups F and G2a. The sample size was nevertheless too small to rule out that E1b1b was part of this culture. E-V13 was later associated with the ancient Greek expansion and colonisation. Outside of the Balkans and Central Europe, it is particularly common in southern Italy, Cyprus and southern France, all part of the Classical ancient Greek world.

1. The E-L17 subclade has been found from Ukraine to Portugal and from Sardinia to England.2. The E-L143 subclade has only been found in England.3. The E-L241 subclade has been found in the Czech Republic and England.4. The E-L540 subclade has been found in Germany, the Czech Republic, Poland, Belarus and Sweden.

Distribution of haplogroup E-V13 in Europe, the Middle East & North Africa

E-V22 is found primarily in western Ethiopia, northern Egypt and in the southern Levant. In Europe it is therefore associated with the Phoenicians and the Jews, in addition to the propagation of agriculture. The Phoenicians could have disseminated E-V22 to Sicily, Sardinia, southern Spain and the Maghreb, and the Jews to Greece and mainland Italy and Spain. However, the Mediterranean route for the diffusion of agriculture (see map above) went through the exact same regions. It is therefore impossible to know at present which of the two periods (Neolithic or Classical Antiquity) played the stronger role in the spread of V22 around the Mediterranean.

E-V12 is the most common subclade of M78 in southern Egypt (over 40% of the population), while its V32 subclade is the dominant paternal lineage in Somalia, southern Ethiopia and northern Kenya. The moderate presence of V12* in the Near East and across Europe (except Nordic countries) indicates that it was a minor Neolithic lineage accompanying E-V13. V32 has not been found outside Northeast Africa.

E-V65 is found chiefly in North Africa, with a maximum frequency (20-30%) observed in Lybia, Tunisia and northern Morocco. The absence of V65 from the Horn of Africa means that it would have originated in North Africa. V65 has also been found at lower frequencies (0.5% to 5%) in Egypt, Greece, southern Italy, Sicily and more interestingly among the Sardinians and the Basques, two population isolates with strong affinities with the Neolithic and Mesolithic populations of Europe. However, V65 has not been found in the Levant, the Balkans or in non-Mediterranean Europe, which disproves a Neolithic dispersal. Its strongly North African distribution and very minor presence in parts of southern Europe with historical links to North Africa would rather suggest that this lineage was brought to southern Europe by immigrants from North Africa. In the case of Italy this could have taken place any time from the Phoenician/Carthaginian period (c. 1000-146 BCE) until the Vandal Kingdom. In Greece, V65 could have come from the ancient colonies of Cyrenaica. In Iberia, V65 could have crossed the Strait of Gibraltar any time since the late Paleolithic.

E1b1b1b1a (M81)

E-M81 probably originated in the Horn of Africa, although its presence is very limited there nowadays (1.5% in Somalia, 5% in Sudan). M81 spread throughout North Africa and the Levant and became the dominant lineage of the Berbers of Northwest Africa, almost certainly due to a founder effect. M81 is found at an average frequency of 45% in the Maghreb and Lybia, with peaks at over 60% in Tunisia as well as central and southern Morocco. M81 is also found in Portugal (8%), Spain (4%), as well as in France (0-6%) and Italy (0-4%), where strong regional variations are observed. M81 is especially common in western Iberia, notably Extremadura (15.5%), Andalusia (13.5%), southern Portugal (11%), north-west Castille (10%) and Galicia (10%). The highest percentage of E-M81 in Europe is found among the Pasiegos (30%, n=101), an isolated community living in the mountains of Cantabria.

Note the resemblance between the distribution of E-M81 and the African admixture from the Dodecad project.

Distribution of haplogroup E-M81 in Europe, the Middle East & North Africa

E1b1b1b2a (M123)

E-M123 is most commonly found in Ethiopia (5-20%), where it appears to have originated. Its main subclade E-M34 probably emerged in the southern Levant, where it reaches its maximum frequency (10-12% among the Palestinians and the Jews, 8% among the Bedouins, 5% in Lebanon), then expanded in every direction across North Africa (3-5%), the Middle East and South Asia, Anatolia (3-6%) and southern Europe, particularly Italy (1 to 8%). The distribution of E-M123 matches almost exactly the early expansion of farming in the Middle East (see map above) during the Neolithic period, but not so much in Europe, where the only possible association with a Neolithic culture is as a minor haplogroup of the Cardium Pottery culture. E-M123 is conspicuously absent from the part of the Balkans where E-V13 reaches its maximum (Thessaly, Albania, Kosovo) as well as from most Slavic countries, which is strong evidence that M123 wa not associated with the Thessalian Neolithic and its offshoots, like the Linear Pottery culture.

In Europe E-M123 is only observed at frequencies over 2.5% in southern Italy, in the Spanish region Extremadura (4%), and the Balearic islands of Ibiza and Minorca (average 10%). E-M123 could have been brought to the Mediterranean coasts of Europe by the Phoenicians, and to Italy by the Etruscans (from Anatolia). The Romans might have contributed to spreading it around their empire at low frequencies.

Distribution of haplogroup E-M123 in Europe, the Middle East & North Africa